658 commits

Author	SHA1	Message	Date
James Fellows Yates	dd94895f16	remove quotes	2022-02-10 11:22:45 +01:00
James Fellows Yates	39c2d9b25b	Oops	2022-02-10 11:19:16 +01:00
James Fellows Yates	c0ee3225ad	Add times for 365d	2022-02-10 11:02:52 +01:00
Thiseas C. Lamnidis	fa4075c2a0	Removed all time limits	2022-02-10 10:00:18 +01:00
James A. Fellows Yates	64355b84d2	Merge pull request #325 from jfy133/eva-update ... Read add empty BAM exit code for qualimap 255 for eager @ EVA	2022-02-08 11:28:36 +01:00
James A. Fellows Yates	2b06293f64	Read add empty BAM exit code for qualitmap 255	2022-02-08 11:15:17 +01:00
James A. Fellows Yates	8d286e3b69	Merge pull request #324 from jfy133/eva-update ... New attempt of workaround SGE + Java incompatibility for eager @ EVA	2022-02-06 20:02:03 +01:00
James A. Fellows Yates	8c5a54ac9f	Update conf/pipeline/eager/eva.config	2022-02-06 19:37:53 +01:00
James A. Fellows Yates	aa525c6ebf	Allow exit code 1 retry for all java processes	2022-02-06 09:07:53 +01:00
phue	7bf6f284fa	cbe: lower the threshold for switching to m queue	2022-02-04 10:33:00 +01:00
phue	49810a69b3	cbe: add gpu support ... just in case.. note that this will need --nv in containerOptions in order to mount cuda libs into the container	2022-02-04 10:31:58 +01:00
phue	52b6f7da21	update anaconda module ... not sure why a binary distribution needs a buildenv at all, but well	2022-02-04 10:18:59 +01:00
James A. Fellows Yates	81fe720b00	Update eva.config	2022-02-04 09:31:33 +01:00
James A. Fellows Yates	86a9042eac	Update eva.config	2022-02-04 09:25:01 +01:00
James A. Fellows Yates	50aafc6410	Update eva.config	2022-02-03 17:03:10 +01:00
James A. Fellows Yates	8739aabbf0	Bump markduplicates by default	2022-02-02 08:00:13 +01:00
Harshil Patel	9792226f5c	Update genomes.config	2022-01-27 12:45:41 +00:00
Harshil Patel	cd6b8e0f17	Add --nextclade_dataset params	2022-01-17 16:51:55 +00:00
Harshil Patel	f26c465bd4	Add Nextclade genome details to viralrecon genome config	2022-01-17 11:27:10 +00:00
James A. Fellows Yates	5fd5c43906	Update eva.config	2022-01-14 07:03:05 +01:00
Maxime U. Garcia	61682f33b3	Merge pull request #310 from nf-core/praveenraj2018-patch-1 ... Updated sentieon version through a new module file	2022-01-10 12:04:20 +01:00
ameynert	0f56588acc	Added memory & cluster options specification for eddie sarek config	2022-01-06 10:15:34 +00:00
praveenraj2018	53ab5ee34f	Updated sentieon version through a new module file ... A local module file has been created to run the latest version of Sentieon. Doing this change, as the new version of Sentieon has only a dependency library update, hence it should not break the Sentieon pipeline. Tested locally with a test.conf having the new process block.	2021-12-21 15:21:59 +01:00
Kevin Brick	1abb1c2d95	Merge pull request #309 from kevbrick/master ... Added config for NIH Biowulf Cluster	2021-12-20 13:05:19 -05:00
Kevin Brick	82c7d553a7	Update bind-paths	2021-12-20 11:29:09 -05:00
Kevin Brick	87e4ece034	Add files via upload	2021-12-17 00:36:51 -05:00
Venkat Malladi	306c802b4e	Fix name of Params	2021-12-16 09:27:23 -06:00
praveenraj2018	0557f4e062	Renamed star_index directory	2021-12-14 21:15:12 +01:00
Maxime U. Garcia	5e92e2ef11	Update conf/pipeline/rnavar/munin.config	2021-12-14 16:10:31 +01:00
Praveen	cc1fe5b5a0	Addressed review feedback	2021-12-14 03:58:54 +01:00
Praveen	b4d5330c0e	Added rnavar pipeline config for Munin	2021-12-14 03:52:37 +01:00
James A. Fellows Yates	55f452d81e	Update eva.config	2021-12-07 09:27:28 +01:00
James Fellows Yates	e8252ad61c	Reintroduce bionode8, bump overhead for flagstat	2021-12-03 08:36:31 +01:00
James Fellows Yates	06b40798c0	Exclude bionode8	2021-12-02 10:35:35 +01:00
Phil Ewels	4785ceccba	Merge pull request #245 from ikeller/unibe_ibu ... Unibe ibu	2021-11-19 00:56:25 +01:00
Phil Ewels	291fcb20a5	Merge pull request #297 from vsmalladi/azure ... Add in template for Azure Workflow	2021-11-19 00:55:54 +01:00
Venkat Malladi	72ccd44ad6	Remove storage name.	2021-11-18 17:52:51 -06:00
Venkat Malladi	ed4c1d5f22	Remove work_dir option.	2021-11-18 17:52:24 -06:00
Phil Ewels	e090bbd5fe	Merge pull request #241 from asafpr/master ... replaced owner in JAX	2021-11-19 00:03:11 +01:00
Phil Ewels	a26b3bf1e3	Merge branch 'master' into unibe_ibu	2021-11-19 00:02:30 +01:00
Phil Ewels	15080d958e	Merge pull request #283 from aunderwo/master ... change max_time diretcive in the correct place	2021-11-19 00:00:52 +01:00
Venkat Malladi	13a8d7aebe	Fix spelling.	2021-11-18 15:51:12 -06:00
Venkat Malladi	845a9ce971	Update Readme with more inforamtion on the options.	2021-11-18 15:47:27 -06:00
Venkat Malladi	219244f1b4	Add in sample datastorage for Illumina Platinum genomes.	2021-11-18 15:28:34 -06:00
Venkat Malladi	b1a9c2e4c6	Add in fake key.	2021-11-18 15:20:59 -06:00
Venkat Malladi	a8075ee938	Fix configuration to pass.	2021-11-18 15:15:23 -06:00
Venkat Malladi	237f91a3b7	Add in minmum config for azure.	2021-11-18 14:51:39 -06:00
Harshil Patel	a098ad9e06	Add Chris as main contact at The Crick	2021-11-03 11:11:05 +00:00
Phil Ewels	501db6bd2b	Update conf/uppmax.config ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2021-11-02 23:55:27 +01:00
Phil Ewels	c842ca70a7	Address review comments	2021-11-02 13:32:19 +01:00